A spell or ability that counters spells can still target spells that can't be countered. When that spell or ability resolves, the uncounterable spell won't be countered, but any additional effects of the countering spell or ability will still happen.

Allosaurus Shepherd's last ability overwrites all previous effects that set the affected creatures' power and/or toughness to specific values. Other effects that set these characteristics to specific values that start to apply after the ability resolves will overwrite that part of the effect.

Effects that modify an affected creature's power or toughness without setting it will apply no matter when they started to take effect. The same is true for counters that change the creature's power or toughness.

The affected creatures don't lose any abilities when they become Dinosaurs.